Segger statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

Segger specifications

Information


Unique identifier OMICS_26710
Name Segger
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A threshold.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
Chimera
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Additional information


http://people.csail.mit.edu/gdp/segger/home.php https://sourceforge.net/projects/segger/ http://www.cgl.ucsf.edu/chimera/data/segger-howto-jun2010/segger.html

Publication for Segger

Segger citations

 (46)
call_split

Structure of a human cap dependent 48S translation pre initiation complex

2018
Nucleic Acids Res
PMCID: 5861459
PMID: 29401259
DOI: 10.1093/nar/gky054
call_split See protocol

[…] Volumes obtained by RELION were segmented in Chimera using the SEGGER tool (,). The atomic models of 40S, tRNAi and eIF2 subunits from the mammalian 48S model (), atomic models of different eIF3 subunits () as well as the crystal structure of Nasonia vitripennis […]

library_books

Enhancing Time Synchronization Support in Wireless Sensor Networks

2017
PMCID: 5751738
PMID: 29261113
DOI: 10.3390/s17122956

[…] alue stored in its memory address (bits 4–8 of for the fine tune and bits 9–12 for the coarse-grain tune).To support C coding and programming, IAR Embedded Workbench software was used together with a Segger J-Link, a debug probe containing a JTAG interface.A connectivity test demo comes preprogrammed in the sensor node. This software was adapted to match the purposes of the designed experiments. […]

call_split

Cryo‐EM reconstruction of Type VI secretion system baseplate and sheath distal end

2017
PMCID: 5813253
PMID: 29255010
DOI: 10.15252/embj.201797103
call_split See protocol

[…] th Resmap (Kucukelbir et al, ).To perform focused refinement of the connector protein region, we low‐pass filtered the refined baseplate map to 80 Å and generated a small mask around TssK region with Segger (Pintilie et al, ) in UCSF Chimera (Pettersen et al, ; Goddard et al, ). Mask was prepared for RELION2.1 with relion_mask_create with extended width and soft edge of five pixels. The subsequent […]

call_split

Insights into the structure and assembly of a bacterial cellulose secretion system

2017
Nat Commun
PMCID: 5727187
PMID: 29234007
DOI: 10.1038/s41467-017-01523-2
call_split See protocol

[…] The three-dimensional structure reconstructions were displayed in UCSF Chimera and segmentation of the volumes was performed with the SEGGER module implemented in the package. Volumetric analysis was also performed in UCSF Chimera with average protein density of 0.81 Da per Å3 used for the volume-to-mass conversion after adjusting t […]

library_books

Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection

2017
Nat Commun
PMCID: 5717097
PMID: 29209037
DOI: 10.1038/s41467-017-02049-3

[…] The crystal structure of pb6 was rigidly fitted in the tube density using the 'fit in map' option in Chimera . This original fit was used to guide segmentation of the map using Segger . Isolated densities corresponding to a monomer was then used to build the missing loop (loop β3–β4, residues 38–67) using Coot and model the structural features rearranged in the tube assembl […]

library_books

Structural Transitions of the Conserved and Metastable Hantaviral Glycoprotein Envelope

2017
J Virol
PMCID: 5640846
PMID: 28835498
DOI: 10.1128/JVI.00378-17

[…] LV cryo-electron tomography (ET) reconstruction, as previously described for PUUV Gn (). In short, the fitting was performed in the segmented density map of TULV using the fit-to-segments function of Segger () in Chimera (). The crystal structure was converted to density by low-pass filtering to 16-Å resolution with 2.7-Å grid spacing. Subsequently, 1,000 evenly rotated fits were considered for ea […]

Citations

Looking to check out a full list of citations?

Segger institution(s)
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
Segger funding source(s)
Supported by NIH grants (P41GM103832 and R01GM079429).

Segger reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Segger